Batch effect when analysing data in Osprey

Dear @admin @mmikkel,

I analysed two cohorts in July 2023 in Osprey as separate batches (I am not sure of the version but it was the most recent version at that time). I have just analysed these cohorts again with a third cohort after my study completed, with all 3 cohorts batched and run together in a single .json file.

Originally, the median of every metabolite was higher in one of the cohorts compared to the other, which I was suspicious of. I have re-run all 3 cohorts together recently (Osprey 2.9.0), those differences have disappeared.

Can you think why running the cohorts as separate batches seemed to introduce batch differences in the results? The .json code run both times looked similar to below, with additional scans, run with

MRSCont = RunOspreyJob('path/to/job/file/osprey.json');

{
	"seqType": "unedited",
	"dataScenario": "invivo",
	"MM3coModel": "3to2MM",
	"FWHMMM3co": "",
	"SpecReg": "RobSpecReg",
	"SubSpecAlignment": "L2Norm",
	"UnstableWater": "0",
	"saveLCM": "0",
	"savejMRUI": "0",
	"saveVendor": "0",
	"saveNII": "0",
	"savePDF": "0",
	"method": "Osprey",
	"ECCmetab": "1",
	"ECCmm": "1",
	"includeMetabs": ["default"],
	"style": "Separate",
	"lolim_range": "0.5",
	"uplim_range": "4.0",
	"lolim_rangew": "2.0",
	"uplim_rangew": "7.4",
	"bLineKnotSpace": "0.4",
	"fitMM": "1",
  	"files": [
    "scan_1.dat",
    "scan_2.dat",
    "scan_3.dat"...],
  	"files_ref": [
    "scan_1_water_ref.dat",
    "scan_2_water_ref.dat",
	"scan_3_water_ref.dat"...],
  	"files_nii": [
    "anat_scan_1.nii",
    "anat_scan_2.nii",
	"anat_scan_3.nii"...],
	"file_stat": [""],
  	"outputFolder": ["outputfolder"]
}

Many thanks,
James

Not really, sorry. Can you post all the job files you used for the different analyses?

Thanks for the reply. Yes of course - could I send them to you privately?

Sure - goeltzs1 [at) jh (dot] edu.